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		<title>Identification - Fragment search</title>
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<h1>Fragment search</h1>

<h2>Description</h2>

<p>
This method identifies fragment peaks using MS/MS scan data. 
Fragment ions are usually produced from another, bigger ion, in the ionization source.
Such additional signals represent an undesired noise.
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<p>
Fragments are identified by 2 conditions: 1) the retention time of the original ion and the fragment ion should be same and 
2) the MS/MS pattern of the original ion must be found in the data set and is must contain a peak with the same mass as the fragment ion.
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<img src="fragmentSearch.png">
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<h4>Method parameters</h4>
<dl>

<dt>RT tolerance</dt>
<dd>Maximum allowed retention time difference to set a relationship between peaks</dd>

<dt>m/z tolerance of MS2 data</dt>
<dd>Tolerance value of the m/z difference between peaks in MS/MS scans</dd>

<dt>Max fragment peak height</dt>
<dd>Maximum height of the recognized fragment peak, relative to the main peak</dd>

<dt>Min MS2 peak height</dt>
<dd>Minimum absolute intensity of the MS2 fragment peak. Signals below this level will be ignored.</dd>

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